Problem at Selecting Points after Extruding
There are several things to keep in mind in your case.

First, it seems you're holding Ctrl while selecting vertices. This means you select these vertices and every vertice located along the shortest path between them.

To select only 2 vertices you should hold Shift while clicking on the vertices.



Second, you have double vertices in your mesh, at least those which are selected. Select all, use W and in the menu choose Remove Doubles. Read similar question here.